From c58ccd73951b2000a7a254fb36bbd9f0733db6cd Mon Sep 17 00:00:00 2001
From: Johannes Ranke
Date: Mon, 12 May 2025 22:16:10 +0200
Subject: Check and test locally
---
docs/reference/AIC.mmkin.html | 2 +-
docs/reference/CAKE_export.html | 2 +-
docs/reference/D24_2014.html | 2 +-
docs/reference/DFOP.solution.html | 2 +-
docs/reference/Extract.mmkin.html | 2 +-
docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html | 2 +-
docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html | 2 +-
docs/reference/FOCUS_2006_HS_ref_A_to_F.html | 2 +-
docs/reference/FOCUS_2006_SFO_ref_A_to_F.html | 2 +-
docs/reference/FOCUS_2006_datasets.html | 2 +-
docs/reference/FOMC.solution.html | 2 +-
docs/reference/HS.solution.html | 2 +-
docs/reference/IORE.solution.html | 2 +-
docs/reference/NAFTA_SOP_2015.html | 2 +-
docs/reference/NAFTA_SOP_Attachment.html | 2 +-
docs/reference/SFO.solution.html | 2 +-
docs/reference/SFORB.solution.html | 2 +-
docs/reference/add_err.html | 2 +-
docs/reference/anova.saem.mmkin.html | 2 +-
docs/reference/aw.html | 2 +-
docs/reference/check_failed.html | 2 +-
docs/reference/confint.mkinfit.html | 6 +++---
docs/reference/create_deg_func.html | 10 ++++-----
docs/reference/dimethenamid_2018.html | 12 +++++------
docs/reference/ds_mixed.html | 2 +-
docs/reference/endpoints.html | 2 +-
docs/reference/experimental_data_for_UBA.html | 2 +-
docs/reference/f_time_norm_focus.html | 2 +-
docs/reference/focus_soil_moisture.html | 2 +-
docs/reference/get_deg_func.html | 2 +-
docs/reference/hierarchical_kinetics.html | 2 +-
docs/reference/illparms.html | 2 +-
docs/reference/ilr.html | 2 +-
docs/reference/index.html | 2 +-
docs/reference/intervals.saem.mmkin.html | 2 +-
docs/reference/llhist.html | 2 +-
docs/reference/loftest.html | 2 +-
docs/reference/logLik.mkinfit.html | 2 +-
docs/reference/logLik.saem.mmkin.html | 2 +-
docs/reference/logistic.solution.html | 2 +-
docs/reference/lrtest.mkinfit.html | 2 +-
docs/reference/max_twa_parent.html | 2 +-
docs/reference/mccall81_245T.html | 2 +-
docs/reference/mean_degparms.html | 2 +-
docs/reference/mhmkin.html | 2 +-
docs/reference/mixed.html | 2 +-
docs/reference/mkin_long_to_wide.html | 2 +-
docs/reference/mkin_wide_to_long.html | 2 +-
docs/reference/mkinds.html | 2 +-
docs/reference/mkindsg.html | 2 +-
docs/reference/mkinerrmin.html | 2 +-
docs/reference/mkinerrplot.html | 2 +-
docs/reference/mkinfit.html | 28 ++++++++++++-------------
docs/reference/mkinmod.html | 7 ++++---
docs/reference/mkinparplot.html | 2 +-
docs/reference/mkinplot.html | 2 +-
docs/reference/mkinpredict.html | 10 ++++-----
docs/reference/mkinresplot.html | 2 +-
docs/reference/mmkin.html | 6 +++---
docs/reference/multistart.html | 2 +-
docs/reference/nafta.html | 2 +-
docs/reference/nlme.html | 2 +-
docs/reference/nlme.mmkin.html | 2 +-
docs/reference/nobs.mkinfit.html | 2 +-
docs/reference/parms.html | 2 +-
docs/reference/parplot.html | 2 +-
docs/reference/plot.mixed.mmkin.html | 2 +-
docs/reference/plot.mkinfit.html | 2 +-
docs/reference/plot.mmkin.html | 2 +-
docs/reference/plot.nafta.html | 2 +-
docs/reference/read_spreadsheet.html | 2 +-
docs/reference/reexports.html | 2 +-
docs/reference/residuals.mkinfit.html | 2 +-
docs/reference/saem.html | 14 ++++++-------
docs/reference/schaefer07_complex_case.html | 2 +-
docs/reference/set_nd_nq.html | 2 +-
docs/reference/sigma_twocomp.html | 2 +-
docs/reference/status.html | 2 +-
docs/reference/summary.mkinfit.html | 10 ++++-----
docs/reference/summary.mmkin.html | 4 ++--
docs/reference/summary.nlme.mmkin.html | 14 ++++++-------
docs/reference/summary.saem.mmkin.html | 12 +++++------
docs/reference/summary_listing.html | 2 +-
docs/reference/synthetic_data_for_UBA_2014.html | 12 +++++------
docs/reference/test_data_from_UBA_2014.html | 2 +-
docs/reference/transform_odeparms.html | 2 +-
docs/reference/update.mkinfit.html | 2 +-
87 files changed, 147 insertions(+), 146 deletions(-)
(limited to 'docs/reference')
diff --git a/docs/reference/AIC.mmkin.html b/docs/reference/AIC.mmkin.html
index 516e6009..5bc4200f 100644
--- a/docs/reference/AIC.mmkin.html
+++ b/docs/reference/AIC.mmkin.html
@@ -9,7 +9,7 @@ same dataset.">
mkin
- 1.2.9
+ 1.2.10
#saemix::plot(f_dmta_saem_tc$so, plot.type = "convergence")
summary(f_dmta_saem_tc)
#> saemix version used for fitting: 3.3
-#> mkin version used for pre-fitting: 1.2.9
-#> R version used for fitting: 4.4.2
-#> Date of fit: Thu Feb 13 14:56:10 2025
-#> Date of summary: Thu Feb 13 14:56:10 2025
+#> mkin version used for pre-fitting: 1.2.10
+#> R version used for fitting: 4.5.0
+#> Date of fit: Mon May 12 20:21:22 2025
+#> Date of summary: Mon May 12 20:21:22 2025
#>
#> Equations:
#> d_DMTA/dt = - k_DMTA * DMTA
@@ -199,7 +199,7 @@ specific pieces of information in the comments.
#>
#> Model predictions using solution type deSolve
#>
-#> Fitted in 295.43 s
+#> Fitted in 303.226 s
#> Using 300, 100 iterations and 9 chains
#>
#> Variance model: Two-component variance function
diff --git a/docs/reference/ds_mixed.html b/docs/reference/ds_mixed.html
index 37c49191..5208f9a4 100644
--- a/docs/reference/ds_mixed.html
+++ b/docs/reference/ds_mixed.html
@@ -9,7 +9,7 @@ the 'dataset_generation' directory.">
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html
index 23c550ca..502b0603 100644
--- a/docs/reference/endpoints.html
+++ b/docs/reference/endpoints.html
@@ -15,7 +15,7 @@ advantage that the SFORB model can also be used for metabolites.">
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/experimental_data_for_UBA.html b/docs/reference/experimental_data_for_UBA.html
index d1329e21..8556fcfb 100644
--- a/docs/reference/experimental_data_for_UBA.html
+++ b/docs/reference/experimental_data_for_UBA.html
@@ -63,7 +63,7 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/f_time_norm_focus.html b/docs/reference/f_time_norm_focus.html
index c318b762..9e688da7 100644
--- a/docs/reference/f_time_norm_focus.html
+++ b/docs/reference/f_time_norm_focus.html
@@ -9,7 +9,7 @@ in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369).">mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/focus_soil_moisture.html b/docs/reference/focus_soil_moisture.html
index 3b07a5ea..305aa407 100644
--- a/docs/reference/focus_soil_moisture.html
+++ b/docs/reference/focus_soil_moisture.html
@@ -9,7 +9,7 @@ corresponds to pF2, MWHC to pF 1 and 1/3 bar to pF 2.5.">
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/get_deg_func.html b/docs/reference/get_deg_func.html
index 6b296b87..ad1b1c82 100644
--- a/docs/reference/get_deg_func.html
+++ b/docs/reference/get_deg_func.html
@@ -7,7 +7,7 @@
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/hierarchical_kinetics.html b/docs/reference/hierarchical_kinetics.html
index 85cd2644..5c59b749 100644
--- a/docs/reference/hierarchical_kinetics.html
+++ b/docs/reference/hierarchical_kinetics.html
@@ -21,7 +21,7 @@ includes them.'>
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/illparms.html b/docs/reference/illparms.html
index cbe48623..f79ee876 100644
--- a/docs/reference/illparms.html
+++ b/docs/reference/illparms.html
@@ -15,7 +15,7 @@ without parameter transformations is used.">
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html
index 7aa6379f..cd817e3e 100644
--- a/docs/reference/ilr.html
+++ b/docs/reference/ilr.html
@@ -9,7 +9,7 @@ transformations.">
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 191fbe04..8076a478 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -7,7 +7,7 @@
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/intervals.saem.mmkin.html b/docs/reference/intervals.saem.mmkin.html
index 3a8cdb5d..08f65cfc 100644
--- a/docs/reference/intervals.saem.mmkin.html
+++ b/docs/reference/intervals.saem.mmkin.html
@@ -7,7 +7,7 @@
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/llhist.html b/docs/reference/llhist.html
index 01299b04..a739c846 100644
--- a/docs/reference/llhist.html
+++ b/docs/reference/llhist.html
@@ -9,7 +9,7 @@ original fit is shown as a red vertical line.">
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/loftest.html b/docs/reference/loftest.html
index 97b48751..136256f7 100644
--- a/docs/reference/loftest.html
+++ b/docs/reference/loftest.html
@@ -13,7 +13,7 @@ lrtest.default from the lmtest package.">
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html
index eddf1f8f..04f38684 100644
--- a/docs/reference/logLik.mkinfit.html
+++ b/docs/reference/logLik.mkinfit.html
@@ -15,7 +15,7 @@ the error model.">
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/logLik.saem.mmkin.html b/docs/reference/logLik.saem.mmkin.html
index 8cc985a8..b32d2f9a 100644
--- a/docs/reference/logLik.saem.mmkin.html
+++ b/docs/reference/logLik.saem.mmkin.html
@@ -7,7 +7,7 @@
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html
index f03f0c70..00af94e9 100644
--- a/docs/reference/logistic.solution.html
+++ b/docs/reference/logistic.solution.html
@@ -9,7 +9,7 @@ an increasing rate constant, supposedly caused by microbial growth">mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/lrtest.mkinfit.html b/docs/reference/lrtest.mkinfit.html
index 17ed11c6..bffae5f3 100644
--- a/docs/reference/lrtest.mkinfit.html
+++ b/docs/reference/lrtest.mkinfit.html
@@ -15,7 +15,7 @@ and can be expressed by fixing the parameters of the other.">
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html
index 453f801a..6af12d05 100644
--- a/docs/reference/max_twa_parent.html
+++ b/docs/reference/max_twa_parent.html
@@ -15,7 +15,7 @@ soil section of the FOCUS guidance.">
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index bb0e36cf..866b093a 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -11,7 +11,7 @@
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/mean_degparms.html b/docs/reference/mean_degparms.html
index e9c78767..9320abbd 100644
--- a/docs/reference/mean_degparms.html
+++ b/docs/reference/mean_degparms.html
@@ -7,7 +7,7 @@
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/mhmkin.html b/docs/reference/mhmkin.html
index 26bfd34b..8b249f77 100644
--- a/docs/reference/mhmkin.html
+++ b/docs/reference/mhmkin.html
@@ -13,7 +13,7 @@ mixed-effects model fitting functions.">
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/mixed.html b/docs/reference/mixed.html
index 9bdd620d..089635f6 100644
--- a/docs/reference/mixed.html
+++ b/docs/reference/mixed.html
@@ -7,7 +7,7 @@
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html
index 4bdbbc64..9f4dcfb0 100644
--- a/docs/reference/mkin_long_to_wide.html
+++ b/docs/reference/mkin_long_to_wide.html
@@ -11,7 +11,7 @@ variable and several dependent variables as columns.">
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html
index bcc303d1..37963f44 100644
--- a/docs/reference/mkin_wide_to_long.html
+++ b/docs/reference/mkin_wide_to_long.html
@@ -11,7 +11,7 @@ mkinfit.">
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html
index 488c0c2f..3c905b02 100644
--- a/docs/reference/mkinds.html
+++ b/docs/reference/mkinds.html
@@ -13,7 +13,7 @@ provided by this package come as mkinds objects nevertheless.">
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/mkindsg.html b/docs/reference/mkindsg.html
index b314a5f8..92d5cd12 100644
--- a/docs/reference/mkindsg.html
+++ b/docs/reference/mkindsg.html
@@ -13,7 +13,7 @@ dataset if no data are supplied.">
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html
index 26cc19f7..3dbcc4b8 100644
--- a/docs/reference/mkinerrmin.html
+++ b/docs/reference/mkinerrmin.html
@@ -9,7 +9,7 @@ the chi-squared test as defined in the FOCUS kinetics report from 2006.">
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/mkinerrplot.html b/docs/reference/mkinerrplot.html
index bcd4285b..b217c154 100644
--- a/docs/reference/mkinerrplot.html
+++ b/docs/reference/mkinerrplot.html
@@ -15,7 +15,7 @@ using the argument show_errplot = TRUE.">
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 5af8eaaf..bc27e81f 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -23,7 +23,7 @@ likelihood function.">
mkin
- 1.2.9
+ 1.2.10
@@ -366,17 +366,17 @@ Degradation Data. Environments 6(12) 124
# Use shorthand notation for parent only degradation
fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
summary(fit)
-#> mkin version used for fitting: 1.2.9
-#> R version used for fitting: 4.4.2
-#> Date of fit: Thu Feb 13 14:56:49 2025
-#> Date of summary: Thu Feb 13 14:56:49 2025
+#> mkin version used for fitting: 1.2.10
+#> R version used for fitting: 4.5.0
+#> Date of fit: Mon May 12 20:22:04 2025
+#> Date of summary: Mon May 12 20:22:04 2025
#>
#> Equations:
#> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
#>
#> Model predictions using solution type analytical
#>
-#> Fitted using 222 model solutions performed in 0.014 s
+#> Fitted using 222 model solutions performed in 0.027 s
#>
#> Error model: Constant variance
#>
@@ -517,9 +517,9 @@ Degradation Data. Environments 6(12) 124
solution_type = "analytical"))
}
#> test relative elapsed
-#> 3 analytical 1.000 0.227
-#> 2 eigen 1.930 0.438
-#> 1 deSolve_compiled 1.991 0.452
+#> 3 analytical 1.000 0.256
+#> 2 eigen 1.898 0.486
+#> 1 deSolve_compiled 2.000 0.512
# }
# Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO
@@ -545,10 +545,10 @@ Degradation Data. Environments 6(12) 124
summary(fit.FOMC_SFO.tc, data = FALSE)
#> Warning: NaNs produced
#> Warning: diag(V) had non-positive or NA entries; the non-finite result may be dubious
-#> mkin version used for fitting: 1.2.9
-#> R version used for fitting: 4.4.2
-#> Date of fit: Thu Feb 13 14:56:53 2025
-#> Date of summary: Thu Feb 13 14:56:53 2025
+#> mkin version used for fitting: 1.2.10
+#> R version used for fitting: 4.5.0
+#> Date of fit: Mon May 12 20:22:10 2025
+#> Date of summary: Mon May 12 20:22:10 2025
#>
#> Equations:
#> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -557,7 +557,7 @@ Degradation Data. Environments 6(12) 124
#>
#> Model predictions using solution type deSolve
#>
-#> Fitted using 4062 model solutions performed in 0.751 s
+#> Fitted using 4062 model solutions performed in 0.809 s
#>
#> Error model: Two-component variance function
#>
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index 9ddbdc59..b4b303a5 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -15,7 +15,7 @@ components.">
mkin
- 1.2.9
+ 1.2.10
@@ -290,7 +290,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media
m1 = mkinsub("SFO", full_name = "Metabolite M1"),
name = "SFO_SFO", dll_dir = DLL_dir, unload = TRUE, overwrite = TRUE)
#> Temporary DLL for differentials generated and loaded
-#> Copied DLL from /tmp/RtmpUBdk0y/file210eb9601bdd53.so to /home/jranke/.local/share/mkin/SFO_SFO.so
+#> Copied DLL from /tmp/Rtmph4D0tb/file1385e349a06fa9.so to /home/jranke/.local/share/mkin/SFO_SFO.so
# Now we can save the model and restore it in a new session
saveRDS(SFO_SFO.2, file = "~/SFO_SFO.rds")
# Terminate the R session here if you would like to check, and then do
@@ -303,6 +303,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media
SFO_SFO <- mkinmod(
parent = mkinsub("SFO", "m1"),
m1 = mkinsub("SFO"), verbose = TRUE)
+#> Setting PKG_CPPFLAGS to -DR_NO_REMAP
#> Program source:
#> 1: #include <R.h>
#> 2:
@@ -343,7 +344,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media
#> })
#> return(predicted)
#> }
-#> <environment: 0x55555a37aab8>
+#> <environment: 0x5555585b89c0>
# If we have several parallel metabolites
# (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)
diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html
index 57f536e0..6a081056 100644
--- a/docs/reference/mkinparplot.html
+++ b/docs/reference/mkinparplot.html
@@ -9,7 +9,7 @@ mkinfit.">
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html
index b5c84645..40478f12 100644
--- a/docs/reference/mkinplot.html
+++ b/docs/reference/mkinplot.html
@@ -9,7 +9,7 @@ plot.mkinfit.">
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index fc656e43..8dc08187 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -11,7 +11,7 @@ kinetic parameters and initial values for the state variables.">
mkin
- 1.2.9
+ 1.2.10
@@ -353,10 +353,10 @@ as these always return mapped output.
solution_type = "analytical", use_compiled = FALSE)[201,])
}
#> test relative elapsed
-#> 2 deSolve_compiled 1 0.002
-#> 4 analytical 1 0.002
-#> 1 eigen 4 0.008
-#> 3 deSolve 32 0.064
+#> 2 deSolve_compiled 1.0 0.002
+#> 4 analytical 1.0 0.002
+#> 1 eigen 4.5 0.009
+#> 3 deSolve 35.0 0.070
# \dontrun{
# Predict from a fitted model
diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html
index 97b24dbf..d1d37b44 100644
--- a/docs/reference/mkinresplot.html
+++ b/docs/reference/mkinresplot.html
@@ -13,7 +13,7 @@ argument show_residuals = TRUE.">
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index 66ea275d..4675a9d3 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -9,7 +9,7 @@ datasets specified in its first two arguments.">
mkin
- 1.2.9
+ 1.2.10
@@ -158,10 +158,10 @@ plotting.
time_default
#> user system elapsed
-#> 1.608 0.866 0.732
+#> 2.423 1.112 1.111
time_1
#> user system elapsed
-#> 1.964 0.016 1.980
+#> 2.655 0.036 2.691
endpoints(fits.0[["SFO_lin", 2]])
#> $ff
diff --git a/docs/reference/multistart.html b/docs/reference/multistart.html
index af5f614e..825e3210 100644
--- a/docs/reference/multistart.html
+++ b/docs/reference/multistart.html
@@ -17,7 +17,7 @@ mixed-effects models by Duchesne et al (2021).">
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/nafta.html b/docs/reference/nafta.html
index 07dc0f42..aa2ab7ca 100644
--- a/docs/reference/nafta.html
+++ b/docs/reference/nafta.html
@@ -15,7 +15,7 @@ order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP.">
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/nlme.html b/docs/reference/nlme.html
index 8bf352af..190ac359 100644
--- a/docs/reference/nlme.html
+++ b/docs/reference/nlme.html
@@ -13,7 +13,7 @@ datasets. They are used internally by the nlme.mmkin() method.">
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/nlme.mmkin.html b/docs/reference/nlme.mmkin.html
index 4f124b07..ba0b0f16 100644
--- a/docs/reference/nlme.mmkin.html
+++ b/docs/reference/nlme.mmkin.html
@@ -11,7 +11,7 @@ have been obtained by fitting the same model to a list of datasets.">mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/nobs.mkinfit.html b/docs/reference/nobs.mkinfit.html
index 3cdfc619..d94f4a34 100644
--- a/docs/reference/nobs.mkinfit.html
+++ b/docs/reference/nobs.mkinfit.html
@@ -7,7 +7,7 @@
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/parms.html b/docs/reference/parms.html
index 46b0bb31..f51455c9 100644
--- a/docs/reference/parms.html
+++ b/docs/reference/parms.html
@@ -11,7 +11,7 @@ without considering the error structure that was assumed for the fit.">mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/parplot.html b/docs/reference/parplot.html
index 30523983..54e3880f 100644
--- a/docs/reference/parplot.html
+++ b/docs/reference/parplot.html
@@ -11,7 +11,7 @@ or by their medians as proposed in the paper by Duchesne et al. (2021).">
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/plot.mixed.mmkin.html b/docs/reference/plot.mixed.mmkin.html
index 838265d8..1c3abcaa 100644
--- a/docs/reference/plot.mixed.mmkin.html
+++ b/docs/reference/plot.mixed.mmkin.html
@@ -7,7 +7,7 @@
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html
index 4ce5a914..10c21e2c 100644
--- a/docs/reference/plot.mkinfit.html
+++ b/docs/reference/plot.mkinfit.html
@@ -11,7 +11,7 @@ observed data together with the solution of the fitted model.">
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html
index 572731a7..7f35d790 100644
--- a/docs/reference/plot.mmkin.html
+++ b/docs/reference/plot.mmkin.html
@@ -11,7 +11,7 @@ the fit of at least one model to the same dataset is shown.">
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/plot.nafta.html b/docs/reference/plot.nafta.html
index 2b2338c6..170599a4 100644
--- a/docs/reference/plot.nafta.html
+++ b/docs/reference/plot.nafta.html
@@ -9,7 +9,7 @@ function (SFO, then IORE, then DFOP).">
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/read_spreadsheet.html b/docs/reference/read_spreadsheet.html
index 173ee608..069b8403 100644
--- a/docs/reference/read_spreadsheet.html
+++ b/docs/reference/read_spreadsheet.html
@@ -17,7 +17,7 @@ factors can be given in columns named 'Temperature' and 'Moisture'.">mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 94ee6f14..f7cacc84 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -29,7 +29,7 @@ intervals, nlme
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/residuals.mkinfit.html b/docs/reference/residuals.mkinfit.html
index cf2f62bb..4da7194c 100644
--- a/docs/reference/residuals.mkinfit.html
+++ b/docs/reference/residuals.mkinfit.html
@@ -7,7 +7,7 @@
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/saem.html b/docs/reference/saem.html
index 7146875f..2d02fd77 100644
--- a/docs/reference/saem.html
+++ b/docs/reference/saem.html
@@ -11,7 +11,7 @@ Expectation Maximisation algorithm (SAEM).">
mkin
- 1.2.9
+ 1.2.10
@@ -395,10 +395,10 @@ using mmkin.
summary(f_saem_dfop_sfo, data = TRUE)
#> saemix version used for fitting: 3.3
-#> mkin version used for pre-fitting: 1.2.9
-#> R version used for fitting: 4.4.2
-#> Date of fit: Thu Feb 13 14:59:07 2025
-#> Date of summary: Thu Feb 13 14:59:07 2025
+#> mkin version used for pre-fitting: 1.2.10
+#> R version used for fitting: 4.5.0
+#> Date of fit: Mon May 12 20:24:36 2025
+#> Date of summary: Mon May 12 20:24:36 2025
#>
#> Equations:
#> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -413,7 +413,7 @@ using mmkin.
#>
#> Model predictions using solution type analytical
#>
-#> Fitted in 3.96 s
+#> Fitted in 3.747 s
#> Using 300, 100 iterations and 10 chains
#>
#> Variance model: Constant variance
@@ -695,7 +695,7 @@ using mmkin.
#>
#> In above message, R1 = 91
#>
-#> Error in deSolve::lsoda(y = odeini, times = outtimes, func = lsoda_func, :
+#> Error in deSolve::lsoda(y = odeini, times = outtimes_deSolve, func = lsoda_func, :
#> illegal input detected before taking any integration steps - see written message
#anova(
diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html
index c11e4ec5..732b71ff 100644
--- a/docs/reference/schaefer07_complex_case.html
+++ b/docs/reference/schaefer07_complex_case.html
@@ -11,7 +11,7 @@
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/set_nd_nq.html b/docs/reference/set_nd_nq.html
index 3ee21a41..238a2f6f 100644
--- a/docs/reference/set_nd_nq.html
+++ b/docs/reference/set_nd_nq.html
@@ -15,7 +15,7 @@ it automates the proposal of Boesten et al (2015).">
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/sigma_twocomp.html b/docs/reference/sigma_twocomp.html
index 5c9fb8b8..b3be95e9 100644
--- a/docs/reference/sigma_twocomp.html
+++ b/docs/reference/sigma_twocomp.html
@@ -9,7 +9,7 @@ dependence of the measured value \(y\):">
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/status.html b/docs/reference/status.html
index bf77c36d..d7a6d669 100644
--- a/docs/reference/status.html
+++ b/docs/reference/status.html
@@ -7,7 +7,7 @@
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index 86663890..aa3f6bf0 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -15,7 +15,7 @@ values.">
mkin
- 1.2.9
+ 1.2.10
@@ -191,10 +191,10 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
Examples
summary(mkinfit("SFO", FOCUS_2006_A, quiet = TRUE))
-#> mkin version used for fitting: 1.2.9
-#> R version used for fitting: 4.4.2
-#> Date of fit: Thu Feb 13 15:01:12 2025
-#> Date of summary: Thu Feb 13 15:01:12 2025
+#> mkin version used for fitting: 1.2.10
+#> R version used for fitting: 4.5.0
+#> Date of fit: Mon May 12 20:26:43 2025
+#> Date of summary: Mon May 12 20:26:43 2025
#>
#> Equations:
#> d_parent/dt = - k_parent * parent
diff --git a/docs/reference/summary.mmkin.html b/docs/reference/summary.mmkin.html
index bf48a2a6..d1f90296 100644
--- a/docs/reference/summary.mmkin.html
+++ b/docs/reference/summary.mmkin.html
@@ -9,7 +9,7 @@ and gives an overview of ill-defined parameters calculated by illparms.">
mkin
- 1.2.9
+ 1.2.10
@@ -113,7 +113,7 @@ and gives an overview of ill-defined parameters calculated by #> false convergence (8)
summary(fits)
#> Error model: Constant variance
-#> Fitted in 0.478 s
+#> Fitted in 0.533 s
#>
#> Status:
#> dataset
diff --git a/docs/reference/summary.nlme.mmkin.html b/docs/reference/summary.nlme.mmkin.html
index 22cecb0d..c4f53a23 100644
--- a/docs/reference/summary.nlme.mmkin.html
+++ b/docs/reference/summary.nlme.mmkin.html
@@ -15,7 +15,7 @@ endpoints such as formation fractions and DT50 values. Optionally
mkin
- 1.2.9
+ 1.2.10
@@ -211,11 +211,11 @@ José Pinheiro and Douglas Bates for the components inherited from nlme
#> iteration limit reached without convergence (10)
f_nlme <- nlme(f_mmkin)
summary(f_nlme, data = TRUE)
-#> nlme version used for fitting: 3.1.166
-#> mkin version used for pre-fitting: 1.2.9
-#> R version used for fitting: 4.4.2
-#> Date of fit: Thu Feb 13 15:01:14 2025
-#> Date of summary: Thu Feb 13 15:01:14 2025
+#> nlme version used for fitting: 3.1.168
+#> mkin version used for pre-fitting: 1.2.10
+#> R version used for fitting: 4.5.0
+#> Date of fit: Mon May 12 20:26:45 2025
+#> Date of summary: Mon May 12 20:26:45 2025
#>
#> Equations:
#> d_parent/dt = - k_parent * parent
@@ -225,7 +225,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme
#>
#> Model predictions using solution type analytical
#>
-#> Fitted in 0.185 s using 4 iterations
+#> Fitted in 0.193 s using 4 iterations
#>
#> Variance model: Two-component variance function
#>
diff --git a/docs/reference/summary.saem.mmkin.html b/docs/reference/summary.saem.mmkin.html
index 4c9f0d17..39cdb471 100644
--- a/docs/reference/summary.saem.mmkin.html
+++ b/docs/reference/summary.saem.mmkin.html
@@ -15,7 +15,7 @@ endpoints such as formation fractions and DT50 values. Optionally
mkin
- 1.2.9
+ 1.2.10
@@ -288,10 +288,10 @@ saemix authors for the parts inherited from saemix.
#> b.1 0.06522297 0.07920531 0.09318766
summary(f_saem_dfop_sfo_2, data = TRUE)
#> saemix version used for fitting: 3.3
-#> mkin version used for pre-fitting: 1.2.9
-#> R version used for fitting: 4.4.2
-#> Date of fit: Thu Feb 13 15:01:30 2025
-#> Date of summary: Thu Feb 13 15:01:30 2025
+#> mkin version used for pre-fitting: 1.2.10
+#> R version used for fitting: 4.5.0
+#> Date of fit: Mon May 12 20:27:02 2025
+#> Date of summary: Mon May 12 20:27:02 2025
#>
#> Equations:
#> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -306,7 +306,7 @@ saemix authors for the parts inherited from saemix.
#>
#> Model predictions using solution type analytical
#>
-#> Fitted in 9.035 s
+#> Fitted in 9.206 s
#> Using 300, 100 iterations and 10 chains
#>
#> Variance model: Two-component variance function
diff --git a/docs/reference/summary_listing.html b/docs/reference/summary_listing.html
index 01ddec57..8d0c6da5 100644
--- a/docs/reference/summary_listing.html
+++ b/docs/reference/summary_listing.html
@@ -9,7 +9,7 @@ option results = "asis".'>
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/synthetic_data_for_UBA_2014.html b/docs/reference/synthetic_data_for_UBA_2014.html
index b81bbea4..630fade6 100644
--- a/docs/reference/synthetic_data_for_UBA_2014.html
+++ b/docs/reference/synthetic_data_for_UBA_2014.html
@@ -37,7 +37,7 @@ Compare also the code in the example section to see the degradation models.">mkin
- 1.2.9
+ 1.2.10
@@ -240,10 +240,10 @@ Compare also the code in the example section to see the degradation models."> plot_sep(fit)
summary(fit)
-#> mkin version used for fitting: 1.2.9
-#> R version used for fitting: 4.4.2
-#> Date of fit: Thu Feb 13 15:01:40 2025
-#> Date of summary: Thu Feb 13 15:01:40 2025
+#> mkin version used for fitting: 1.2.10
+#> R version used for fitting: 4.5.0
+#> Date of fit: Mon May 12 20:27:12 2025
+#> Date of summary: Mon May 12 20:27:12 2025
#>
#> Equations:
#> d_parent/dt = - k_parent * parent
@@ -252,7 +252,7 @@ Compare also the code in the example section to see the degradation models.">#>
#> Model predictions using solution type deSolve
#>
-#> Fitted using 848 model solutions performed in 0.165 s
+#> Fitted using 848 model solutions performed in 0.176 s
#>
#> Error model: Constant variance
#>
diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html
index 2ebbbd96..70608d65 100644
--- a/docs/reference/test_data_from_UBA_2014.html
+++ b/docs/reference/test_data_from_UBA_2014.html
@@ -9,7 +9,7 @@
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index feaf0917..94a9b6a8 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -17,7 +17,7 @@ the ilr transformation is used.">
mkin
- 1.2.9
+ 1.2.10
diff --git a/docs/reference/update.mkinfit.html b/docs/reference/update.mkinfit.html
index e4a2de34..24467b43 100644
--- a/docs/reference/update.mkinfit.html
+++ b/docs/reference/update.mkinfit.html
@@ -13,7 +13,7 @@ override these starting values.">
mkin
- 1.2.9
+ 1.2.10
--
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